Revived test_app.py
Change chroot handling

* Add class args to Chroot()
* Implement checks in app.inio() for chroot variables
* Normalize chroot configuration variables
* Fix tests to reflect changes
* Add --chroot-copy and --chroot-root to build command
Move setting of config defaults to app.init()
Bugfix: The repo command did not use conf.input_path

When using the repo command, the stage directory was determined with
os.getcwd(), and not conf.input_path. This was causing the directory to be made
in the testing directory when writing tests.
Add create argument to tests.util.tem_filepath()
Add dest arg copy_test_project_to_temp()
Change app.init() args in test_existing_precheck()